Changeset 4045
- Timestamp:
- Jun 27, 2019 5:32:56 PM (6 years ago)
- Files:
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- 5 edited
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Tutorials/CalibrationTutorial/CalibrationTutorial.html (modified) (1 diff)
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Tutorials/SeqRefine/SequentialTutorial.htm (modified) (1 diff)
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Tutorials/StartingGSASII/Starting GSAS.htm (modified) (7 diffs)
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trunk/GSASIIctrlGUI.py (modified) (10 diffs)
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trunk/GSASIIdataGUI.py (modified) (3 diffs)
Legend:
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TabularUnified Tutorials/CalibrationTutorial/CalibrationTutorial.html ¶
r3546 r4045 29 29 <p class="c3"><span class="c4 c9">Step 1: Finding Average Difference Between Set Distance and Calibrated Distance</span></p> 30 30 <p class="c5"></p> 31 <p class="c3"><span class="c1">Go to </span><span class="c2">Image Controls </span><span class="c1">for </span><span class="c2">IMG Si_free_dc200_1-00000.tif</span><span class="c1">, </span><span class="c1">and change </span><span class="c2">wavelength</span><span class="c1"> to 0.241689 as determined in part 1. </span><span class="c2">Uncheck</span><span class="c1"> </span><span class="c2">wavelength</span><span class="c1">, and </span><span class="c2">check</span><span class="c1"> </span><span class="c2">Distance</span><span class="c0">. We are doing this because we now have a calibrated wavelength, and we want to calibrate the detector distances. The Image Controls should look like this:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 597.00px; height: 371.00px;"><img alt="" src="images/image9.png" style="width: 749.05px; height: 421.43px; margin-left: -86.03px; margin-top: -13.21px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">In the </span><span class="c2">Image Controls</span><span class="c1"> tab for </span><span class="c2">IMG Si_free_dc200_1-00000.tif</span><span class="c1">, do </span><span class="c2">Calibrate/Recalibrate</span><span class="c1">. Keep doing this until </span><span class="c2">penetration</span><span class="c1"> (under Calibration coefficients) is constant. Usually recalibrating </span><span class="c2">3</span><span class="c0"> times will suffice. Our penetration value converged to 0.1139.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 612.00px; height: 381.00px;"><img alt="" src="images/image40.png" style="width: 769.15px; height: 432.26px; margin-left: -89.35px; margin-top: -12.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1"> </span></p><p class="c3"><span class="c1">The parameters have been adjusted because of recalibration. We want to copy these new parameters to the rest of the images. Go to</span><span class="c2"> Parms/Copy Selected</span><span class="c0">. A window will appear like the one below:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 437.50px; height: 297.56px;"><img alt="" src="images/image2.png" style="width: 919.19px; height: 517.05px; margin-left: -253.37px; margin-top: -94.28px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1"> </span></p><p class="c3"><span class="c1">Scroll down and select </span><span class="c2">varyList (28)</span><span class="c1"> and </span><span class="c2">wavelength (29)</span><span class="c0">. Take notice of what parameters are noted as true and false, such as ‘dist’: True, and ‘wave’: False’, these are what will be refined.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 468.00px; height: 314.00px;"><img alt="" src="images/image6.png" style="width: 987.47px; height: 554.30px; margin-left: -272.61px; margin-top: -102.65px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">OK</span><span class="c1">. A new screen will appear. Select </span><span class="c2">Set All</span><span class="c0"> to select all images</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 244.50px; height: 323.84px;"><img alt="" src="images/image38.png" style="width: 1010.38px; height: 568.34px; margin-left: -396.71px; margin-top: -105.25px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1"> and click </span><span class="c2">OK</span><span class="c0">.</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Scroll to the bottom of the Data Tree and go to </span><span class="c2">Image Controls</span><span class="c1"> for the last image, </span><span class="c2">IMG Si_free_dc1300_1-00000.tif</span><span class="c0">. All of the Image Control parameters set for the first image have been copied to the rest of the images.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 602.00px; height: 376.00px;"><img alt="" src="images/image23.png" style="width: 754.78px; height: 424.36px; margin-left: -87.46px; margin-top: -12.09px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Do </span><span class="c2">Calibrate/Recalibrate All/Set All</span><span class="c1">. </span><span class="c1">This recalibration finds the offset of between the set distance and actual distance</span><span class="c1">. The amount of time that recalibrating takes is dependant on the number of pixels. So if there are a large number of pixels for that particular image, then recalibrating will take longer to complete. After the calibration, go to the table under the </span><span class="c2">Sequential image calibration results</span><span class="c0"> tab in the GSAS data tree.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 646.50px; height: 404.18px;"><img alt="" src="images/image25.png" style="width: 810.07px; height: 456.16px; margin-left: -92.17px; margin-top: -13.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">From this table we see a column for the calibrated distance (dist) and set distance (setdist) that was recorded when the data was being collected. Although the values are similar, there are slight differences for each image. We will now set up an equation to find the differences between the dist and setdist values.</span></p><p class="c3"><span class="c1">In the GSAS-II Data Tree, go to </span><span class="c2">Sequential image calibration results/Pseudo Vars/Add formula. </span><span class="c0">A popup window will appear.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 483.50px; height: 263.13px;"><img alt="" src="images/image42.png" style="width: 1026.20px; height: 577.24px; margin-left: -379.89px; margin-top: -174.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Type in the equation </span><span class="c2">a-b</span><span class="c1"> next to </span><span class="c2">New PseudoVar=</span><span class="c2"> </span><span class="c1">and press </span><span class="c2">Validate. </span><span class="c0">The popup window change and allow you to enter variable types.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 436.50px; height: 237.68px;"><img alt="" src="images/image1.png" style="width: 932.79px; height: 524.70px; margin-left: -346.81px; margin-top: -159.95px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Set the </span><span class="c2">a</span><span class="c1"> variable as </span><span class="c2">global</span><span class="c0"> and a drop down bar will appear</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 453.50px; height: 209.06px;"><img alt="" src="images/image19.png" style="width: 959.27px; height: 539.56px; margin-left: -355.11px; margin-top: -198.30px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c2">dist Global dist</span><span class="c1">. Next, set the b variable as </span><span class="c2">global</span><span class="c0"> as well and another drop down menu will appear.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 459.50px; height: 207.16px;"><img alt="" src="images/image20.png" style="width: 971.96px; height: 546.73px; margin-left: -359.81px; margin-top: -199.38px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c2">setdist Global setdist</span><span class="c1">. Then press</span><span class="c2"> OK</span><span class="c1">. A new column called </span><span class="c2">a-b</span><span class="c1"> will now appear in the table under </span><span class="c4 c2">Sequential image calibration results. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 606.50px; height: 360.49px;"><img alt="" src="images/image29.png" style="width: 759.95px; height: 427.47px; margin-left: -96.21px; margin-top: -34.10px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Double click on the new column: </span><span class="c2">a-b </span><span class="c0">so it is highlighted.</span></p><p class="c3"><span class="c1">Next, go to the graph called </span><span class="c2">sequential refinement</span><span class="c0"> in the plot window. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 426.50px; height: 396.77px;"><img alt="" src="images/image18.png" style="width: 806.47px; height: 453.64px; margin-left: -226.17px; margin-top: -23.26px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">K</span><span class="c1"> (at the bottom of the screen)</span><span class="c2">/Select x-axis/setdist. </span><span class="c0">Now the x axis is the set distance.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 471.50px; height: 439.97px;"><img alt="" src="images/image35.png" style="width: 894.27px; height: 503.03px; margin-left: -250.80px; margin-top: -25.80px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Next we want to calculate the average. In a perfect world, the graph should be constant at </span><span class="c2">0</span><span class="c1"> with no error, but at very close and very far distances this is not possible. Select the </span><span class="c2">a-b</span><span class="c1"> column once again. Go to </span><span class="c2">columns/rows/c</span><span class="c2">ompute average</span><span class="c2">. </span><span class="c0">Look at the terminal window.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 303.00px; height: 21.00px;"><img alt="" src="images/image26.png" style="width: 1264.48px; height: 719.55px; margin-left: -212.77px; margin-top: -569.50px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">In the terminal window, we can see the calculated </span><span class="c2">average</span><span class="c1"> of -0.123759 and magnitude of +/- 0.287854 for </span><span class="c2">error</span><span class="c0">. The error in this case, is very high (around 0.3).</span></p><p class="c3"><span class="c1">Notice that the first and last few images are the least accurate because they are either too close or too far away from the detector to gather an accurate reading.</span></p><p class="c3"><span class="c1">Therefore, go to </span><span class="c2">Sequential image calibration results</span><span class="c1"> and unclick image </span><span class="c2">use</span><span class="c0"> for images 200-400 and 1050-1300. The table should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 611.50px; height: 365.22px;"><img alt="" src="images/image36.png" style="width: 767.76px; height: 430.17px; margin-left: -98.43px; margin-top: -34.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">To calculate the average again, select the </span><span class="c2">a-b</span><span class="c1"> column again by double clicking on the column header then go to </span><span class="c2">Columns/Rows/Compute average</span><span class="c1">. The </span><span class="c2">terminal</span><span class="c0"> window will show:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 333.00px; height: 25.00px;"><img alt="" src="images/image15.png" style="width: 1419.88px; height: 807.30px; margin-left: -236.54px; margin-top: -637.10px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0"> The magnitude of error of +/- 0.045307 is much smaller and more desirable. Therefore we feel more confident saying that the average distance between set distance and calibrated distance is -0.167927</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c4 c9">Step 2: Integrating the Calibrated Data</span></p><p class="c3"><span class="c1">This next step involves integration of the data. Go to </span><span class="c2">Image Controls</span><span class="c1"> for the first image, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1"> and then go to the </span><span class="c2">GSAS-II plot window</span><span class="c0">. Select the tab with the powder data rings. Notice the beamstop and pin dial. In the final integration, we do not want to use these areas, so we will work on excluding these from the integration.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 519.00px; height: 483.00px;"><img alt="" src="images/image37.png" style="width: 519.00px; height: 483.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1"> </span></p><p class="c3"><span class="c1">In the </span><span class="c2">GSAS-II data tree</span><span class="c1">, go to </span><span class="c2">Image Controls</span><span class="c1"> for the first image, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">. We will be working in the </span><span class="c2">Integration coefficients </span><span class="c1">area. Click </span><span class="c2">Show integration limits?</span><span class="c0">. The plot should show the area that is to be integrated.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 467.50px; height: 434.82px;"><img alt="" src="images/image33.png" style="width: 886.69px; height: 498.76px; margin-left: -224.51px; margin-top: -17.05px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Zoom in </span><span class="c1">on the beamstop (bullseye of rings)</span><span class="c0"> so we can make sure to exclude this from our final integration.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 436.50px; height: 404.66px;"><img alt="" src="images/image11.png" style="width: 827.89px; height: 465.69px; margin-left: -209.63px; margin-top: -17.25px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Change the</span><span class="c2"> </span><span class="c2">inner 2-theta</span><span class="c1"> to a smaller value of </span><span class="c2">0.8</span><span class="c0"> to only exclude the small beamstop in the middle and not the surrounding data.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 466.50px; height: 435.40px;"><img alt="" src="images/image4.png" style="width: 882.11px; height: 496.19px; margin-left: -391.58px; margin-top: -29.69px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click the </span><span class="c2">home</span><span class="c1"> button to see all the rings. Drag the mouse to the rights side of the image. As the mouse moves to the right, </span><span class="c2">2-theta</span><span class="c0"> changes at the bottom of the screen. Note the outer 2-theta value when the mouse stops at the edge of the screen. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 600.00px; height: 560.00px;"><img alt="" src="images/image5.gif" style="width: 600.00px; height: 560.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Type this value (we used</span><span class="c1"> </span><span class="c1">44.80</span><span class="c1">) into the </span><span class="c2">Outer 2-theta</span><span class="c1"> box. Check the </span><span class="c2">Do full integration?</span><span class="c0"> Box.</span></p><p class="c3"><span class="c0">The image controls screen should look like this:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 622.98px; height: 386.50px;"><img alt="" src="images/image27.png" style="width: 781.38px; height: 439.03px; margin-left: -108.31px; margin-top: -12.51px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">And the plot showing the integration limits should look like:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 434.50px; height: 402.80px;"><img alt="" src="images/image3.png" style="width: 824.10px; height: 463.55px; margin-left: -217.91px; margin-top: -19.81px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see from the image, the inner and outer angles that we entered gave us a good integration area around the powder rings.</span></p><p class="c3"><span class="c1">At this point, we are going to cut out the beamstop, which yields poor intensity data. So, remove the </span><span class="c2">Do full integration?</span><span class="c0"> Box.</span></p><p class="c3"><span class="c1">To exclude the beamstop we will adjust the start/end azimuth degrees. Make the </span><span class="c2">Start azimuth 5, </span><span class="c1">and </span><span class="c2">End azimuth </span><span class="c1">either</span><span class="c2"> 355 </span><span class="c1">or</span><span class="c2"> -5.0</span><span class="c0"> (it does not matter). The image controls window should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 642.50px; height: 399.15px;"><img alt="" src="images/image12.png" style="width: 803.45px; height: 451.94px; margin-left: -109.44px; margin-top: -11.59px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">And the plot showing the integration limits should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 437.50px; height: 405.78px;"><img alt="" src="images/image14.png" style="width: 827.27px; height: 465.45px; margin-left: -218.75px; margin-top: -18.57px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see, the beamstop will now be excluded from our integration of the data.</span></p><p class="c3"><span class="c1">At this point it is a good idea to use </span><span class="c4 c2">Save project.</span></p>31 <p class="c3"><span class="c1">Go to </span><span class="c2">Image Controls </span><span class="c1">for </span><span class="c2">IMG Si_free_dc200_1-00000.tif</span><span class="c1">, </span><span class="c1">and change </span><span class="c2">wavelength</span><span class="c1"> to 0.241689 as determined in part 1. </span><span class="c2">Uncheck</span><span class="c1"> </span><span class="c2">wavelength</span><span class="c1">, and </span><span class="c2">check</span><span class="c1"> </span><span class="c2">Distance</span><span class="c0">. We are doing this because we now have a calibrated wavelength, and we want to calibrate the detector distances. The Image Controls should look like this:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 597.00px; height: 371.00px;"><img alt="" src="images/image9.png" style="width: 749.05px; height: 421.43px; margin-left: -86.03px; margin-top: -13.21px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">In the </span><span class="c2">Image Controls</span><span class="c1"> tab for </span><span class="c2">IMG Si_free_dc200_1-00000.tif</span><span class="c1">, do </span><span class="c2">Calibrate/Recalibrate</span><span class="c1">. Keep doing this until </span><span class="c2">penetration</span><span class="c1"> (under Calibration coefficients) is constant. Usually recalibrating </span><span class="c2">3</span><span class="c0"> times will suffice. Our penetration value converged to 0.1139.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 612.00px; height: 381.00px;"><img alt="" src="images/image40.png" style="width: 769.15px; height: 432.26px; margin-left: -89.35px; margin-top: -12.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1"> </span></p><p class="c3"><span class="c1">The parameters have been adjusted because of recalibration. We want to copy these new parameters to the rest of the images. Go to</span><span class="c2"> Parms/Copy Selected</span><span class="c0">. A window will appear like the one below:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 437.50px; height: 297.56px;"><img alt="" src="images/image2.png" style="width: 919.19px; height: 517.05px; margin-left: -253.37px; margin-top: -94.28px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1"> </span></p><p class="c3"><span class="c1">Scroll down and select </span><span class="c2">varyList (28)</span><span class="c1"> and </span><span class="c2">wavelength (29)</span><span class="c0">. Take notice of what parameters are noted as true and false, such as ‘dist’: True, and ‘wave’: False’, these are what will be refined.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 468.00px; height: 314.00px;"><img alt="" src="images/image6.png" style="width: 987.47px; height: 554.30px; margin-left: -272.61px; margin-top: -102.65px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">OK</span><span class="c1">. A new screen will appear. Select </span><span class="c2">Set All</span><span class="c0"> to select all images</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 244.50px; height: 323.84px;"><img alt="" src="images/image38.png" style="width: 1010.38px; height: 568.34px; margin-left: -396.71px; margin-top: -105.25px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1"> and click </span><span class="c2">OK</span><span class="c0">.</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Scroll to the bottom of the Data Tree and go to </span><span class="c2">Image Controls</span><span class="c1"> for the last image, </span><span class="c2">IMG Si_free_dc1300_1-00000.tif</span><span class="c0">. All of the Image Control parameters set for the first image have been copied to the rest of the images.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 602.00px; height: 376.00px;"><img alt="" src="images/image23.png" style="width: 754.78px; height: 424.36px; margin-left: -87.46px; margin-top: -12.09px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Do </span><span class="c2">Calibrate/Recalibrate All/Set All</span><span class="c1">. </span><span class="c1">This recalibration finds the offset of between the set distance and actual distance</span><span class="c1">. The amount of time that recalibrating takes is dependant on the number of pixels. So if there are a large number of pixels for that particular image, then recalibrating will take longer to complete. After the calibration, go to the table under the </span><span class="c2">Sequential image calibration results</span><span class="c0"> tab in the GSAS data tree.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 646.50px; height: 404.18px;"><img alt="" src="images/image25.png" style="width: 810.07px; height: 456.16px; margin-left: -92.17px; margin-top: -13.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">From this table we see a column for the calibrated distance (dist) and set distance (setdist) that was recorded when the data was being collected. Although the values are similar, there are slight differences for each image. We will now set up an equation to find the differences between the dist and setdist values.</span></p><p class="c3"><span class="c1">In the GSAS-II Data Tree, go to </span><span class="c2">Sequential image calibration results/Pseudo Vars/Add formula. </span><span class="c0">A popup window will appear.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 483.50px; height: 263.13px;"><img alt="" src="images/image42.png" style="width: 1026.20px; height: 577.24px; margin-left: -379.89px; margin-top: -174.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Type in the equation </span><span class="c2">a-b</span><span class="c1"> next to </span><span class="c2">New PseudoVar=</span><span class="c2"> </span><span class="c1">and press </span><span class="c2">Validate. </span><span class="c0">The popup window change and allow you to enter variable types.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 436.50px; height: 237.68px;"><img alt="" src="images/image1.png" style="width: 932.79px; height: 524.70px; margin-left: -346.81px; margin-top: -159.95px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Set the </span><span class="c2">a</span><span class="c1"> variable as </span><span class="c2">global</span><span class="c0"> and a drop down bar will appear</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 453.50px; height: 209.06px;"><img alt="" src="images/image19.png" style="width: 959.27px; height: 539.56px; margin-left: -355.11px; margin-top: -198.30px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c2">dist Global dist</span><span class="c1">. Next, set the b variable as </span><span class="c2">global</span><span class="c0"> as well and another drop down menu will appear.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 459.50px; height: 207.16px;"><img alt="" src="images/image20.png" style="width: 971.96px; height: 546.73px; margin-left: -359.81px; margin-top: -199.38px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c2">setdist Global setdist</span><span class="c1">. Then press</span><span class="c2"> OK</span><span class="c1">. A new column called </span><span class="c2">a-b</span><span class="c1"> will now appear in the table under </span><span class="c4 c2">Sequential image calibration results. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 606.50px; height: 360.49px;"><img alt="" src="images/image29.png" style="width: 759.95px; height: 427.47px; margin-left: -96.21px; margin-top: -34.10px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Double click on the new column: </span><span class="c2">a-b </span><span class="c0">so it is highlighted.</span></p><p class="c3"><span class="c1">Next, go to the graph called </span><span class="c2">sequential refinement</span><span class="c0"> in the plot window. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 426.50px; height: 396.77px;"><img alt="" src="images/image18.png" style="width: 806.47px; height: 453.64px; margin-left: -226.17px; margin-top: -23.26px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">K</span><span class="c1"> (at the bottom of the screen)</span><span class="c2">/Select x-axis/setdist. </span><span class="c0">Now the x axis is the set distance.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 471.50px; height: 439.97px;"><img alt="" src="images/image35.png" style="width: 894.27px; height: 503.03px; margin-left: -250.80px; margin-top: -25.80px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Next we want to calculate the average. In a perfect world, the graph should be constant at </span><span class="c2">0</span><span class="c1"> with no error, but at very close and very far distances this is not possible. Select the </span><span class="c2">a-b</span><span class="c1"> column once again. Go to </span><span class="c2">columns/rows/c</span><span class="c2">ompute average</span><span class="c2">. </span><span class="c0">Look at the terminal window.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 303.00px; height: 21.00px;"><img alt="" src="images/image26.png" style="width: 1264.48px; height: 719.55px; margin-left: -212.77px; margin-top: -569.50px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">In the terminal window, we can see the calculated </span><span class="c2">average</span><span class="c1"> of -0.123759 and magnitude of +/- 0.287854 for </span><span class="c2">error</span><span class="c0">. The error in this case, is very high (around 0.3).</span></p><p class="c3"><span class="c1">Notice that the first and last few images are the least accurate because they are either too close or too far away from the detector to gather an accurate reading.</span></p><p class="c3"><span class="c1">Therefore, go to </span><span class="c2">Sequential image calibration results</span><span class="c1"> and unclick image </span><span class="c2">use</span><span class="c0"> for images 200-400 and 1050-1300. The table should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 611.50px; height: 365.22px;"><img alt="" src="images/image36.png" style="width: 767.76px; height: 430.17px; margin-left: -98.43px; margin-top: -34.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">To calculate the average again, select the </span><span class="c2">a-b</span><span class="c1"> column again by double clicking on the column header then go to </span><span class="c2">Columns/Rows/Compute average</span><span class="c1">. The </span><span class="c2">terminal</span><span class="c0"> window will show:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 333.00px; height: 25.00px;"><img alt="" src="images/image15.png" style="width: 1419.88px; height: 807.30px; margin-left: -236.54px; margin-top: -637.10px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0"> The magnitude of error of +/- 0.045307 is much smaller and more desirable. Therefore we feel more confident saying that the average distance between set distance and calibrated distance is -0.167927</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c4 c9">Step 2: Integrating the Calibrated Data</span></p><p class="c3"><span class="c1">This next step involves integration of the data. Go to </span><span class="c2">Image Controls</span><span class="c1"> for the first image, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1"> and then go to the </span><span class="c2">GSAS-II plot window</span><span class="c0">. Select the tab with the powder data rings. Notice shadowed regions from the beamstop and pin diode. In the final integration, we do not want to use these areas, so we will work on excluding these from the integration.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 519.00px; height: 483.00px;"><img alt="" src="images/image37.png" style="width: 519.00px; height: 483.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span><span class="c1"> </span></p><p class="c3"><span class="c1">In the </span><span class="c2">GSAS-II data tree</span><span class="c1">, go to </span><span class="c2">Image Controls</span><span class="c1"> for the first image, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">. We will be working in the </span><span class="c2">Integration coefficients </span><span class="c1">area. Click </span><span class="c2">Show integration limits?</span><span class="c0">. The plot should show the area that is to be integrated.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 467.50px; height: 434.82px;"><img alt="" src="images/image33.png" style="width: 886.69px; height: 498.76px; margin-left: -224.51px; margin-top: -17.05px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Zoom in </span><span class="c1">on the beamstop (bullseye of rings)</span><span class="c0"> so we can make sure to exclude this from our final integration.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 436.50px; height: 404.66px;"><img alt="" src="images/image11.png" style="width: 827.89px; height: 465.69px; margin-left: -209.63px; margin-top: -17.25px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Change the</span><span class="c2"> </span><span class="c2">inner 2-theta</span><span class="c1"> to a smaller value of </span><span class="c2">0.8</span><span class="c0"> to only exclude the small beamstop in the middle and not the surrounding data.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 466.50px; height: 435.40px;"><img alt="" src="images/image4.png" style="width: 882.11px; height: 496.19px; margin-left: -391.58px; margin-top: -29.69px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click the </span><span class="c2">home</span><span class="c1"> button to see all the rings. Drag the mouse to the rights side of the image. As the mouse moves to the right, </span><span class="c2">2-theta</span><span class="c0"> changes at the bottom of the screen. Note the outer 2-theta value when the mouse stops at the edge of the screen. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 600.00px; height: 560.00px;"><img alt="" src="images/image5.gif" style="width: 600.00px; height: 560.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Type this value (we used</span><span class="c1"> </span><span class="c1">44.80</span><span class="c1">) into the </span><span class="c2">Outer 2-theta</span><span class="c1"> box. Check the </span><span class="c2">Do full integration?</span><span class="c0"> Box.</span></p><p class="c3"><span class="c0">The image controls screen should look like this:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 622.98px; height: 386.50px;"><img alt="" src="images/image27.png" style="width: 781.38px; height: 439.03px; margin-left: -108.31px; margin-top: -12.51px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">And the plot showing the integration limits should look like:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 434.50px; height: 402.80px;"><img alt="" src="images/image3.png" style="width: 824.10px; height: 463.55px; margin-left: -217.91px; margin-top: -19.81px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see from the image, the inner and outer angles that we entered gave us a good integration area around the powder rings.</span></p><p class="c3"><span class="c1">At this point, we are going to cut out the beamstop, which yields poor intensity data. So, remove the </span><span class="c2">Do full integration?</span><span class="c0"> Box.</span></p><p class="c3"><span class="c1">To exclude the beamstop we will adjust the start/end azimuth degrees. Make the </span><span class="c2">Start azimuth 5, </span><span class="c1">and </span><span class="c2">End azimuth </span><span class="c1">either</span><span class="c2"> 355 </span><span class="c1">or</span><span class="c2"> -5.0</span><span class="c0"> (it does not matter). The image controls window should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 642.50px; height: 399.15px;"><img alt="" src="images/image12.png" style="width: 803.45px; height: 451.94px; margin-left: -109.44px; margin-top: -11.59px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">And the plot showing the integration limits should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 437.50px; height: 405.78px;"><img alt="" src="images/image14.png" style="width: 827.27px; height: 465.45px; margin-left: -218.75px; margin-top: -18.57px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see, the beamstop will now be excluded from our integration of the data.</span></p><p class="c3"><span class="c1">At this point it is a good idea to use </span><span class="c4 c2">Save project.</span></p> 32 32 <p class="c5"></p> 33 <p class="c3"><span class="c1">The value for </span><span class="c2">No. 2-theta </span><span class="c1">depends on the number of pixels in the detector. A 1:1 ratio of pixels to No. 2-theta is optimal. </span><span class="c2">2250 </span><span class="c1">for our </span><span class="c2">No. 2-theta </span><span class="c1">value works with our detector size and pixels so we will leave it as is. However, know that that value should be determined by the detector size and number of pixels. </span><span class="c2">Azimuth bins</span><span class="c1"> finds powder patterns every so many degrees. We have it set at </span><span class="c2">1</span><span class="c0">. </span></p><p class="c3"><span class="c1">Go to </span><span class="c2">Parms/Copy Selected </span><span class="c1">and select </span><span class="c2">fullintegrate = false (12), IOtth (15), LRazimuth (16), </span><span class="c1">and</span><span class="c4 c2"> outAzimuths (18), . </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 591.50px; height: 382.88px;"><img alt="" src="images/image10.png" style="width: 765.76px; height: 430.74px; margin-left: -92.04px; margin-top: -6.14px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">OK</span><span class="c0">. </span></p><p class="c3"><span class="c1">A new window appears. Click </span><span class="c2">Set All</span><span class="c0"> </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 234.50px; height: 310.60px;"><img alt="" src="images/image17.png" style="width: 969.06px; height: 545.10px; margin-left: -402.22px; margin-top: -99.39px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Then select </span><span class="c2">OK</span><span class="c0">.</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Now go to the </span><span class="c2">Image Controls</span><span class="c1"> of the last image, </span><span class="c2">Si_free_dc1300_1-00000.tif.</span><span class="c1"> Check </span><span class="c2">Show integration limits?</span><span class="c1"> and change the </span><span class="c2">auto scaler</span><span class="c1"> to </span><span class="c2">95%.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 328.00px; height: 306.00px;"><img alt="" src="images/image16.png" style="width: 624.00px; height: 351.00px; margin-left: -166.00px; margin-top: -14.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see, the 2-theta max angle is off for this image. </span></p><p class="c3"><span class="c1">To fix this, go to the first image, </span><span class="c2">Si_free_dc200_1-00000.tif, </span><span class="c1">then </span><span class="c2">Image Controls,</span><span class="c1"> and finally</span><span class="c2"> Parms/Xfer angles. </span><span class="c1">Select </span><span class="c2">Xfer scaled 2-theta max</span><span class="c1"> and </span><span class="c4 c2">Set All. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 220.50px; height: 385.44px;"><img alt="" src="images/image22.png" style="width: 1083.40px; height: 609.41px; margin-left: -470.52px; margin-top: -92.02px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click</span><span class="c2"> OK. </span><span class="c0">This fixes the maximum angle on all of the images based off the scale we set to the first image. The minimum angle does not change. Here are the correct integration limits for the “1300” image:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 459.50px; height: 428.77px;"><img alt="" src="images/image31.png" style="width: 871.51px; height: 490.23px; margin-left: -230.45px; margin-top: -19.55px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c2">Save project</span><span class="c0"> once again.</span></p><p class="c3"><span class="c1">We have changed the parameters so that GSAS-II does not integrate the beamstop. We will now use a mask to exclude the pin di al. Go back to the first image once again, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">, but this time go to the</span><span class="c2"> Masks </span><span class="c1">section under the data tree</span><span class="c2">. </span><span class="c0">Zoom in on the pin dial in the GSAS-II plots window.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 458.00px; height: 424.00px;"><img alt="" src="images/image21.png" style="width: 868.67px; height: 488.65px; margin-left: -229.70px; margin-top: -20.88px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Do </span><span class="c2">Operations/Create new/Polygon mask</span><span class="c0">. Go to the plot window. Pan the mouse around the pin dial to create a quadrilateral surrounding the light area (pin dial). Click on the plot for each corner of the mask. Lines will be drawn in to connect the corners. Create the mask so that it borders the pin dial.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 581.33px;"><img alt="" src="images/image24.gif" style="width: 624.00px; height: 581.33px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">We have successfully masked the pin dial so it will not be included in our integration.</span></p><p class="c3"><span class="c2 c4">File/Save project.</span></p><p class="c3"><span class="c1">Unzoom on the 2D powder image (can be done by clicking the </span><span class="c2">home</span><span class="c0"> button). </span></p><p class="c3"><span class="c1">We will now check to make sure there is no pin dial in any of the other images. Go to the 2nd image, </span><span class="c2">Si_free_dc250_1-00000.tif/Image Controls. </span><span class="c1">Change the </span><span class="c2">Autoscale</span><span class="c1"> to </span><span class="c4 c2">95%. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 420.50px; height: 389.73px;"><img alt="" src="images/image28.png" style="width: 799.98px; height: 449.99px; margin-left: -210.25px; margin-top: -8.97px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">As we can see, the pin dialdid not show up in this image or any of the following. Therefore, we do not need to do any more masking.</span></p><p class="c3"><span class="c1">Go to </span><span class="c2">Integration/Integrate all.</span><span class="c1"> In the pop-up window, select </span><span class="c4 c2">Set All.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 187.50px; height: 286.26px;"><img alt="" src="images/image34.png" style="width: 893.13px; height: 502.39px; margin-left: -385.02px; margin-top: -91.60px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c4 c2">OK.</span></p><p class="c3"><span class="c1">The data tree now shows PWDR files for each image.</span><span class="c2"> </span><span class="c0">The new graphs show the powder patterns from each of the integrations and should look something like this:</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 459.50px; height: 382.29px;"><img alt="" src="images/image39.png" style="width: 777.04px; height: 437.09px; margin-left: -154.41px; margin-top: -6.23px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">In order to show continuous lines on the graph, press the + key on your keyboard.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 632.33px; height: 524.21px;"><img alt="" src="images/image13.png" style="width: 1069.31px; height: 599.35px; margin-left: -212.49px; margin-top: -8.54px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">To overlap all the cells onto one graph, click on the </span><span class="c2">K/toggle multidata plot</span><span class="c1"> or click </span><span class="c2">m</span><span class="c0"> on your keyboard.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 472.00px; height: 390.00px;"><img alt="" src="images/image8.png" style="width: 796.02px; height: 446.73px; margin-left: -156.91px; margin-top: -6.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">To get a better view of the overlap of data, we zoomed in on the second peak from the left.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 465.50px; height: 386.24px;"><img alt="" src="images/image30.png" style="width: 785.06px; height: 441.60px; margin-left: -154.75px; margin-top: -6.29px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">s</span><span class="c0"> to show a choice of color schemes. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 174.50px; height: 239.51px;"><img alt="" src="images/image41.png" style="width: 1067.53px; height: 600.49px; margin-left: -485.86px; margin-top: -160.81px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">We prefer </span><span class="c2">spectral</span><span class="c1"> (lowercase option). Choose the desired scheme then press</span><span class="c2"> OK</span><span class="c0">.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 536.50px; height: 444.36px;"><img alt="" src="images/image7.png" style="width: 904.80px; height: 508.05px; margin-left: -178.35px; margin-top: -7.24px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">We can tell this is a very accurate calibration because all of the peaks from each image line up very well.</span></p><p class="c3"><span class="c4 c2">File/Save project.</span></p><p class="c3"><span class="c0">We will now save this calibration data into a folder on your computer so it can be used at anytime as a calibrant for measuring an unknown substance. </span></p><p class="c3"><span class="c1">Make a </span><span class="c2">new folder</span><span class="c1"> on your computer (wherever you want to store these calibration files) and call it </span><span class="c2">Image Controls</span><span class="c0">.</span></p><p class="c3"><span class="c1">In any image, go to </span><span class="c2">Image Controls</span><span class="c1">, then go to </span><span class="c2">Parms/Save Multiple Controls </span><span class="c1">and a popup window will appear. Click </span><span class="c2">Set All</span><span class="c0">.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 190.50px; height: 299.14px;"><img alt="" src="images/image32.png" style="width: 928.69px; height: 522.39px; margin-left: -403.32px; margin-top: -93.76px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Then press </span><span class="c4 c2">OK.</span></p><p class="c3"><span class="c1">Click on the newly made folder (</span><span class="c2">Image Controls</span><span class="c1">) where you want to store these files and click </span><span class="c2">Select Folder</span><span class="c0">.</span></p><p class="c3"><span class="c0">This folder will now contain all the image controls and parameters to be used for future measurements.</span></p>33 <p class="c3"><span class="c1">The value for </span><span class="c2">No. 2-theta </span><span class="c1">depends on the number of pixels in the detector. A 1:1 ratio of pixels to No. 2-theta is optimal. </span><span class="c2">2250 </span><span class="c1">for our </span><span class="c2">No. 2-theta </span><span class="c1">value works with our detector size and pixels so we will leave it as is. However, know that that value should be determined by the detector size and number of pixels. </span><span class="c2">Azimuth bins</span><span class="c1"> finds powder patterns every so many degrees. We have it set at </span><span class="c2">1</span><span class="c0">. </span></p><p class="c3"><span class="c1">Go to </span><span class="c2">Parms/Copy Selected </span><span class="c1">and select </span><span class="c2">fullintegrate = false (12), IOtth (15), LRazimuth (16), </span><span class="c1">and</span><span class="c4 c2"> outAzimuths (18), . </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 591.50px; height: 382.88px;"><img alt="" src="images/image10.png" style="width: 765.76px; height: 430.74px; margin-left: -92.04px; margin-top: -6.14px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">OK</span><span class="c0">. </span></p><p class="c3"><span class="c1">A new window appears. Click </span><span class="c2">Set All</span><span class="c0"> </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 234.50px; height: 310.60px;"><img alt="" src="images/image17.png" style="width: 969.06px; height: 545.10px; margin-left: -402.22px; margin-top: -99.39px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Then select </span><span class="c2">OK</span><span class="c0">.</span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c1">Now go to the </span><span class="c2">Image Controls</span><span class="c1"> of the last image, </span><span class="c2">Si_free_dc1300_1-00000.tif.</span><span class="c1"> Check </span><span class="c2">Show integration limits?</span><span class="c1"> and change the </span><span class="c2">auto scaler</span><span class="c1"> to </span><span class="c2">95%.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 328.00px; height: 306.00px;"><img alt="" src="images/image16.png" style="width: 624.00px; height: 351.00px; margin-left: -166.00px; margin-top: -14.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">As we can see, the 2-theta max angle is off for this image. </span></p><p class="c3"><span class="c1">To fix this, go to the first image, </span><span class="c2">Si_free_dc200_1-00000.tif, </span><span class="c1">then </span><span class="c2">Image Controls,</span><span class="c1"> and finally</span><span class="c2"> Parms/Xfer angles. </span><span class="c1">Select </span><span class="c2">Xfer scaled 2-theta max</span><span class="c1"> and </span><span class="c4 c2">Set All. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 220.50px; height: 385.44px;"><img alt="" src="images/image22.png" style="width: 1083.40px; height: 609.41px; margin-left: -470.52px; margin-top: -92.02px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click</span><span class="c2"> OK. </span><span class="c0">This fixes the maximum angle on all of the images based off the scale we set to the first image. The minimum angle does not change. Here are the correct integration limits for the “1300” image:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 459.50px; height: 428.77px;"><img alt="" src="images/image31.png" style="width: 871.51px; height: 490.23px; margin-left: -230.45px; margin-top: -19.55px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3 c5"><span class="c0"></span></p><p class="c3"><span class="c2">Save project</span><span class="c0"> once again.</span></p><p class="c3"><span class="c1">We have changed the parameters so that GSAS-II does not integrate the beamstop. We will now use a mask to exclude the pin diode. Go back to the first image once again, </span><span class="c2">Si_free_dc200_1-00000.tif</span><span class="c1">, but this time go to the</span><span class="c2"> Masks </span><span class="c1">section under the data tree</span><span class="c2">. </span><span class="c0">Zoom in on the pin diode in the GSAS-II plots window.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 458.00px; height: 424.00px;"><img alt="" src="images/image21.png" style="width: 868.67px; height: 488.65px; margin-left: -229.70px; margin-top: -20.88px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Do </span><span class="c2">Operations/Create new/Polygon mask</span><span class="c0">. Go to the plot window. Pan the mouse around the pin diode to create a quadrilateral surrounding the light area (pin diode). Click on the plot for each corner of the mask. Lines will be drawn in to connect the corners. Create the mask so that it borders the pin diode.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 581.33px;"><img alt="" src="images/image24.gif" style="width: 624.00px; height: 581.33px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">We have successfully masked the pin diode so it will not be included in our integration.</span></p><p class="c3"><span class="c2 c4">File/Save project.</span></p><p class="c3"><span class="c1">Unzoom on the 2D powder image (can be done by clicking the </span><span class="c2">home</span><span class="c0"> button). </span></p><p class="c3"><span class="c1">We will now check to make sure there is no pin diode in any of the other images. Go to the 2nd image, </span><span class="c2">Si_free_dc250_1-00000.tif/Image Controls. </span><span class="c1">Change the </span><span class="c2">Autoscale</span><span class="c1"> to </span><span class="c4 c2">95%. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 420.50px; height: 389.73px;"><img alt="" src="images/image28.png" style="width: 799.98px; height: 449.99px; margin-left: -210.25px; margin-top: -8.97px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">As we can see, the pin diode did not show up in this image or any of the following. Therefore, we do not need to do any more masking.</span></p><p class="c3"><span class="c1">Go to </span><span class="c2">Integration/Integrate all.</span><span class="c1"> In the pop-up window, select </span><span class="c4 c2">Set All.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 187.50px; height: 286.26px;"><img alt="" src="images/image34.png" style="width: 893.13px; height: 502.39px; margin-left: -385.02px; margin-top: -91.60px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Select </span><span class="c4 c2">OK.</span></p><p class="c3"><span class="c1">The data tree now shows PWDR files for each image.</span><span class="c2"> </span><span class="c0">The new graphs show the powder patterns from each of the integrations and should look something like this:</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 459.50px; height: 382.29px;"><img alt="" src="images/image39.png" style="width: 777.04px; height: 437.09px; margin-left: -154.41px; margin-top: -6.23px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">In order to show continuous lines on the graph, press the + key on your keyboard.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 632.33px; height: 524.21px;"><img alt="" src="images/image13.png" style="width: 1069.31px; height: 599.35px; margin-left: -212.49px; margin-top: -8.54px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">To overlap all the cells onto one graph, click on the </span><span class="c2">K/toggle multidata plot</span><span class="c1"> or click </span><span class="c2">m</span><span class="c0"> on your keyboard.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 472.00px; height: 390.00px;"><img alt="" src="images/image8.png" style="width: 796.02px; height: 446.73px; margin-left: -156.91px; margin-top: -6.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">To get a better view of the overlap of data, we zoomed in on the second peak from the left.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 465.50px; height: 386.24px;"><img alt="" src="images/image30.png" style="width: 785.06px; height: 441.60px; margin-left: -154.75px; margin-top: -6.29px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Click </span><span class="c2">s</span><span class="c0"> to show a choice of color schemes. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 174.50px; height: 239.51px;"><img alt="" src="images/image41.png" style="width: 1067.53px; height: 600.49px; margin-left: -485.86px; margin-top: -160.81px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">We prefer </span><span class="c2">spectral</span><span class="c1"> (lowercase option). Choose the desired scheme then press</span><span class="c2"> OK</span><span class="c0">.</span></p><p class="c3"><span class="c1"> </span><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 536.50px; height: 444.36px;"><img alt="" src="images/image7.png" style="width: 904.80px; height: 508.05px; margin-left: -178.35px; margin-top: -7.24px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c0">We can tell this is a very accurate calibration because all of the peaks from each image line up very well.</span></p><p class="c3"><span class="c4 c2">File/Save project.</span></p><p class="c3"><span class="c0">We will now save this calibration data into a folder on your computer so it can be used at anytime as a calibrant for measuring an unknown substance. </span></p><p class="c3"><span class="c1">Make a </span><span class="c2">new folder</span><span class="c1"> on your computer (wherever you want to store these calibration files) and call it </span><span class="c2">Image Controls</span><span class="c0">.</span></p><p class="c3"><span class="c1">In any image, go to </span><span class="c2">Image Controls</span><span class="c1">, then go to </span><span class="c2">Parms/Save Multiple Controls </span><span class="c1">and a popup window will appear. Click </span><span class="c2">Set All</span><span class="c0">.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 190.50px; height: 299.14px;"><img alt="" src="images/image32.png" style="width: 928.69px; height: 522.39px; margin-left: -403.32px; margin-top: -93.76px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c1">Then press </span><span class="c4 c2">OK.</span></p><p class="c3"><span class="c1">Click on the newly made folder (</span><span class="c2">Image Controls</span><span class="c1">) where you want to store these files and click </span><span class="c2">Select Folder</span><span class="c0">.</span></p><p class="c3"><span class="c0">This folder will now contain all the image controls and parameters to be used for future measurements.</span></p> 34 34 35 35 <p class="c5"></p> -
TabularUnified Tutorials/SeqRefine/SequentialTutorial.htm ¶
r3918 r4045 2218 2218 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> 2219 2219 2220 <p class=MsoListParagraphCxSpMiddle>Note that the files must be read in in the 2221 sequence they will be processed. This is not an issue here, but for some 2222 sequential refinements, one may need to use multiple Import operations to read 2223 the files in the desired order or rename files so they are listed in the 2224 correct order in the file browser. </p> 2220 <p class=MsoListParagraphCxSpMiddle>Note that the files will be 2221 processed in the order they appear in the tree (or the reverse of that 2222 order, as set in Controls). It will be most convenient if the files 2223 are imported in a logical sequence, which could require multiple 2224 Import operations to read the files in the desired order or to 2225 rename files prior to reading so they are listed in the 2226 correct order in the file browser. If files are not read in the 2227 intended order, it will be necessary to 2228 manually change the positions of the tree items (by dragging them with 2229 the right mouse button pressed). 2230 This is not an issue in this example, since the files are listing in a 2231 zip file in the order they need to be read, but may be of concern 2232 for other cases. 2233 </p> 2225 2234 2226 2235 <p class=MsoListParagraphCxSpMiddle><o:p> </o:p></p> -
TabularUnified Tutorials/StartingGSASII/Starting GSAS.htm ¶
r3552 r4045 1201 1201 <p class=MsoNormal><span class=GramE><b style='mso-bidi-font-weight:normal'><span 1202 1202 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1203 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin' >python</span></b></span><b1203 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin' translate="no">Python</span></b></span><b 1204 1204 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1205 1205 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: … … 1210 1210 mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'><o:p> </o:p></span></b></p> 1211 1211 1212 <p class=MsoNormal>This will work if the default pythonis as described in the1212 <p class=MsoNormal>This will work if the default <span translate="no">Python</span> is as described in the 1213 1213 GSAS-II Wiki pages you found when downloading GSAS-II, otherwise you may have 1214 to enter the correct path for that version of python.</p>1214 to enter the correct path for that version of <span translate="no">Python</span>.</p> 1215 1215 1216 1216 <p class=MsoNormal><o:p> </o:p></p> … … 1230 1230 <p class=MsoNormal><o:p> </o:p></p> 1231 1231 1232 <p class=MsoNormal>When GSAS-II starts, you should see three windows, two of which are almost empty. 1233 The topmost one is a vertically split window; we will refer to this as the <b 1234 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1235 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: 1236 minor-latin'>Data Window</span></b>. The left side will contain a tree-like 1232 When GSAS-II starts, you should see three windows, two of which are almost empty. 1233 The topmost one is a vertically split window; we will refer to this as 1234 the <b><span translate="no">Data</span> <span translate="no">Window</span></b>. The left side will contain a tree-like 1237 1235 outline of your GSAS-II project as you add data, phases, etc. The right side 1238 1236 will contain a display of data depending on your tree item selection; you can … … 1241 1239 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1242 1240 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: 1243 minor-latin' >GSASII Plots</span></b>; this will contain tabbed graphical1241 minor-latin' translate="no">GSASII Plots</span></b>; this will contain tabbed graphical 1244 1242 displays, when appropriate, corresponding to the selected tree item. This may 1245 1243 be a crystal structure, powder pattern plot, etc. The tabs allow you to view … … 1257 1255 of the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1258 1256 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: 1259 minor-latin' >Data Window</span></b>; on a Mac this menu will appear in the1257 minor-latin' translate="no">Data Window</span></b>; on a Mac this menu will appear in the 1260 1258 system menu bar location (usually at the screen top). 1261 1259 The items in the menu bar are separated by a vertical … … 1265 1263 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1266 1264 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-theme-font: 1267 minor-latin' >Data Window</span></b>. On my Windows machine the screen looked1265 minor-latin' translate="no">Data Window</span></b>. On my Windows machine the screen looked 1268 1266 like:</p> 1269 1267 … … 1301 1299 (Exception: image files are not stored in the project; to save space only the 1302 1300 file name is saved.) The console window displays a banner and some information 1303 about the version of pythonand the packages used by GSAS-II. This console1301 about the version of <span translate="no">Python</span> and the packages used by GSAS-II. This console 1304 1302 window will display important information as data processing by GSAS-II 1305 1303 proceeds. You may wish to cut-and-paste parts of this window to another place -
TabularUnified trunk/GSASIIctrlGUI.py ¶
r4039 r4045 5664 5664 def onSetFmtSelection(): 5665 5665 extSel.Clear() 5666 extSel.AppendItems( pwdrReaders[Settings['fmt']].extensionlist)5667 Settings['extStr'] = pwdrReaders[Settings['fmt']].extensionlist[0]5666 extSel.AppendItems(fileReaders[Settings['fmt']].extensionlist) 5667 Settings['extStr'] = fileReaders[Settings['fmt']].extensionlist[0] 5668 5668 extSel.SetSelection(0) 5669 5669 onSetExtSelection() … … 5679 5679 if not os.path.exists(Settings['indir']): 5680 5680 valid = False 5681 if not os.path.exists(Settings['instfile']):5681 if FileTyp == 'pwd' and not os.path.exists(Settings['instfile']): 5682 5682 valid = False 5683 5683 btnstart.Enable(valid) … … 5695 5695 5696 5696 # get a list of existing histograms 5697 PWDRlist = [] 5697 if FileTyp == 'pwd': 5698 treePrfx = 'PWDR ' 5699 else: 5700 treePrfx = 'PDF ' 5701 ReadList = [] 5698 5702 if G2frame.GPXtree.GetCount(): 5699 5703 item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root) 5700 5704 while item: 5701 5705 name = G2frame.GPXtree.GetItemText(item) 5702 if name.startswith( 'PWDR ') and name not in PWDRlist:5703 PWDRlist.append(name)5706 if name.startswith(treePrfx) and name not in ReadList: 5707 ReadList.append(name) 5704 5708 item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie) 5705 Settings[' PWDRlist'] = PWDRlist5706 def RunTimer Loop(event):5709 Settings['ReadList'] = ReadList 5710 def RunTimerPWDR(event): 5707 5711 if GSASIIpath.GetConfigValue('debug'): 5708 5712 import datetime … … 5715 5719 if f in Settings['filesread']: continue 5716 5720 Settings['filesread'].append(f) 5717 rd = pwdrReaders[Settings['fmt']]5721 rd = fileReaders[Settings['fmt']] 5718 5722 rd.ReInitialize() 5719 5723 if not rd.ContentsValidator(f): … … 5758 5762 HistName = 'PWDR '+G2obj.StripUnicode(rd.idstring,'_') 5759 5763 # make new histogram names unique 5760 HistName = G2obj.MakeUniqueLabel(HistName,Settings[' PWDRlist'])5761 Settings[' PWDRlist'].append(HistName)5764 HistName = G2obj.MakeUniqueLabel(HistName,Settings['ReadList']) 5765 Settings['ReadList'].append(HistName) 5762 5766 # put into tree 5763 5767 Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=HistName) … … 5800 5804 print('Warning: CorrectionCode from instprm file not applied') 5801 5805 # code below produces error on Py2.7: unqualified exec is not 5802 # allowed in function 'RunTimerLoop'because it is a nested function5806 # allowed in this function because it is a nested function 5803 5807 # no attempt made to address this. 5804 5808 # … … 5862 5866 G2frame.GPXtree.Expand(Id) 5863 5867 G2frame.GPXtree.SelectItem(Id) 5868 5869 def RunTimerGR(event): 5870 if GSASIIpath.GetConfigValue('debug'): 5871 import datetime 5872 print ("DBG_Timer tick at {:%d %b %Y %H:%M:%S}\n".format(datetime.datetime.now())) 5873 filelist = glob.glob(os.path.join(Settings['indir'],Settings['filter'])) 5874 if not filelist: return 5875 #if GSASIIpath.GetConfigValue('debug'): print(filelist) 5876 Id = None 5877 for f in filelist: 5878 if f in Settings['filesread']: continue 5879 Settings['filesread'].append(f) 5880 rd = fileReaders[Settings['fmt']] 5881 rd.ReInitialize() 5882 if not rd.ContentsValidator(f): 5883 Settings['timer'].Stop() 5884 btnstart.SetLabel('Continue') 5885 G2G.G2MessageBox(dlg,'Error in reading file {}: {}'.format( 5886 f, rd.errors)) 5887 return 5888 #if len(rd.selections) > 1: 5889 # G2fil.G2Print('Warning: Skipping file {}: multibank not yet implemented'.format(f)) 5890 # continue 5891 block = 0 5892 rdbuffer = {} 5893 repeat = True 5894 while repeat: 5895 repeat = False 5896 try: 5897 flag = rd.Reader(f,buffer=rdbuffer, blocknum=block) 5898 except: 5899 flag = False 5900 if flag: 5901 rd.readfilename = f 5902 if rd.warnings: 5903 G2fil.G2Print("Read warning by", rd.formatName, 5904 "reader:", 5905 rd.warnings) 5906 elif not block: 5907 G2fil.G2Print("{} read by Reader {}" 5908 .format(f,rd.formatName)) 5909 else: 5910 G2fil.G2Print("{} block # {} read by Reader {}" 5911 .format(f,block,rd.formatName)) 5912 block += 1 5913 repeat = rd.repeat 5914 else: 5915 G2fil.G2Print("Warning: {} Reader failed to read {}" 5916 .format(rd.formatName,filename)) 5917 if 'phoenix' in wx.version(): 5918 HistName = 'PDF '+rd.idstring 5919 else: 5920 HistName = 'PDF '+G2obj.StripUnicode(rd.idstring,'_') 5921 HistName = G2obj.MakeUniqueLabel(HistName,Settings['ReadList']) 5922 Settings['ReadList'].append(HistName) 5923 # put into tree 5924 Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=HistName) 5925 Ymin = np.min(rd.pdfdata[1]) 5926 Ymax = np.max(rd.pdfdata[1]) 5927 valuesdict = { 5928 'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize), 5929 'Offset':[0.0,0.0],'delOffset':0.02*Ymax, 5930 'Yminmax':[Ymin,Ymax], 5931 } 5932 G2frame.GPXtree.SetItemPyData( 5933 G2frame.GPXtree.AppendItem(Id,text='PDF Controls'), 5934 {'G(R)':[valuesdict,rd.pdfdata,HistName], 5935 'diffGRname':'','diffMult':1.0,'Rmax':Ymax,}) 5936 G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='PDF Peaks'), 5937 {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]}) 5938 5939 # select and show last PWDR file to be read 5940 if Id: 5941 G2frame.EnablePlot = True 5942 G2frame.GPXtree.Expand(Id) 5943 G2frame.GPXtree.SelectItem(Id) 5864 5944 5865 5945 global AutoLoadWindow … … 5871 5951 pass 5872 5952 AutoLoadWindow = None 5873 pwdrReaders = [i for i in G2fil.LoadImportRoutines("pwd", "Powder_Data") 5953 if FileTyp == 'pwd': 5954 fileReaders = [i for i in G2fil.LoadImportRoutines("pwd", "Powder_Data") 5874 5955 if i.scriptable] 5875 fmtchoices = [p.longFormatName for p in pwdrReaders] 5876 Settings['fmt'] = [i for i,v in enumerate(fmtchoices) if 'fxye' in v][0] 5956 fmtchoices = [p.longFormatName for p in fileReaders] 5957 Settings['fmt'] = [i for i,v in enumerate(fmtchoices) if 'fxye' in v][0] 5958 else: 5959 fileReaders = [i for i in G2frame.ImportPDFReaderlist] 5960 # if i.scriptable] 5961 fmtchoices = [p.longFormatName for p in fileReaders] 5962 Settings['fmt'] = 0 5877 5963 Settings['ext'] = 0 5878 5964 Settings['extStr'] = '' … … 5881 5967 Settings['instfile'] = '' 5882 5968 Settings['timer'] = wx.Timer() 5883 Settings['timer'].Bind(wx.EVT_TIMER,RunTimerLoop) 5969 if FileTyp == 'pwd': 5970 Settings['timer'].Bind(wx.EVT_TIMER,RunTimerPWDR) 5971 else: 5972 Settings['timer'].Bind(wx.EVT_TIMER,RunTimerGR) 5884 5973 Settings['filesread'] = [] 5885 5974 dlg = wx.Frame(G2frame,title='Automatic Data Loading', … … 5920 6009 mnsizer.Add(sizer,0,wx.EXPAND) 5921 6010 5922 sizer = wx.BoxSizer(wx.HORIZONTAL) 5923 sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Instrument parameter file from: '),0,wx.ALIGN_CENTER_VERTICAL) 5924 fInp4 = ValidatedTxtCtrl(mnpnl,Settings,'instfile',size=(300,-1), 6011 if FileTyp == 'pwd': 6012 sizer = wx.BoxSizer(wx.HORIZONTAL) 6013 sizer.Add(wx.StaticText(mnpnl, wx.ID_ANY,'Instrument parameter file from: '),0,wx.ALIGN_CENTER_VERTICAL) 6014 fInp4 = ValidatedTxtCtrl(mnpnl,Settings,'instfile',size=(300,-1), 5925 6015 OnLeave=TestInput) 5926 sizer.Add(fInp4,1,wx.ALIGN_CENTER_VERTICAL|wx.EXPAND)5927 btn4 = wx.Button(mnpnl, wx.ID_ANY, "Browse")5928 btn4.Bind(wx.EVT_BUTTON, OnBrowse)5929 sizer.Add(btn4,0,wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)5930 mnsizer.Add(sizer,0,wx.EXPAND)6016 sizer.Add(fInp4,1,wx.ALIGN_CENTER_VERTICAL|wx.EXPAND) 6017 btn4 = wx.Button(mnpnl, wx.ID_ANY, "Browse") 6018 btn4.Bind(wx.EVT_BUTTON, OnBrowse) 6019 sizer.Add(btn4,0,wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL) 6020 mnsizer.Add(sizer,0,wx.EXPAND) 5931 6021 5932 6022 # buttons on bottom -
TabularUnified trunk/GSASIIdataGUI.py ¶
r4040 r4045 1243 1243 #import imp 1244 1244 #imp.reload(G2G) 1245 G2G.AutoLoadFiles(self )1245 G2G.AutoLoadFiles(self,FileTyp='pwd') 1246 1246 self.Bind(wx.EVT_MENU, OnAutoImport, id=item.GetId()) 1247 1247 … … 2375 2375 submenu = wx.Menu() 2376 2376 item = parent.AppendSubMenu(submenu,'PDF G(R) Data','Import PDF G(R) data') 2377 item.Enable(False) # TODO: this does not appear to have ever been made to work2378 2377 for reader in self.ImportPDFReaderlist: 2379 2378 item = submenu.Append(wx.ID_ANY,u'from '+reader.formatName+u' file',reader.longFormatName) 2380 2379 self.ImportMenuId[item.GetId()] = reader 2381 2380 self.Bind(wx.EVT_MENU, self.OnImportPDF, id=item.GetId()) 2381 submenu.AppendSeparator() 2382 item = submenu.Append(wx.ID_ANY,'Auto Import','Import PDF files as found') 2383 def OnAutoImport(event): 2384 #import imp 2385 #imp.reload(G2G) 2386 G2G.AutoLoadFiles(self,FileTyp='gr') 2387 self.Bind(wx.EVT_MENU, OnAutoImport, id=item.GetId()) 2382 2388 # item = submenu.Append(wx.ID_ANY, 2383 2389 # help='Import reflectometry data, use file to try to determine format', … … 2426 2432 'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize), 2427 2433 'Offset':[0.0,0.0],'delOffset':0.02*Ymax, 2428 'Yminmax':[Ymin,Ymax] 2434 'Yminmax':[Ymin,Ymax], 2429 2435 } 2430 2436 self.GPXtree.SetItemPyData( 2431 2437 self.GPXtree.AppendItem(Id,text='PDF Controls'), 2432 {'G(R)':[valuesdict,rd.pdfdata,HistName],'diffGRname':'','diffMult':1.0}) 2438 {'G(R)':[valuesdict,rd.pdfdata,HistName], 2439 'diffGRname':'','diffMult':1.0,'Rmax':Ymax,}) 2433 2440 self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='PDF Peaks'), 2434 2441 {'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
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